# HG changeset patch
# User jfb
# Date 1518119487 18000
# Node ID cf93d3535a31c2082391c170b95be4f170a57a0f
# Parent  a36f9cce16a36a408fb3b0afd277327b098d99f0
Uploaded

diff -r a36f9cce16a3 -r cf93d3535a31 kinatestid_r/Kinatest-R_part1.R
--- a/kinatestid_r/Kinatest-R_part1.R	Thu Feb 08 14:51:12 2018 -0500
+++ b/kinatestid_r/Kinatest-R_part1.R	Thu Feb 08 14:51:27 2018 -0500
@@ -7,9 +7,9 @@
 
 
 
-FILENAME<-"output1"
-FILENAME2<-"output2"
-FILENAME3<-"output3"
+FILENAME<-"output1.csv"
+FILENAME2<-"output2.csv"
+FILENAME3<-"output3.csv"
 
 
 
diff -r a36f9cce16a3 -r cf93d3535a31 kinatestid_r/kinatestid_r.xml
--- a/kinatestid_r/kinatestid_r.xml	Thu Feb 08 14:51:12 2018 -0500
+++ b/kinatestid_r/kinatestid_r.xml	Thu Feb 08 14:51:27 2018 -0500
@@ -1,46 +1,46 @@
-<tool id="kinatestid_r" name="Kinatest-ID 7_to_7" version="0.1.0">
-    <description>calculate optimal substrates</description>
-    <requirements>
-       <requirement type="package">R</requirement>
-    </requirements>
-    <command><![CDATA[
-        ln -s '$__tool_directory__/screener7-7.csv' screener &&
-        ln -s '$substrates' input1 && 
-        ln -s '$negatives' input2 && 
-        ln -s '$SBF' input3 &&
-        Rscript '$__tool_directory__/Kinatest-R_part1.R' &&
-        Rscript '$__tool_directory__/Kinatest-R_part2.R' &&
-        mv output1 output1.csv &&
-        mv output2 output2.csv &&
-        mv output3 output3.csv
-    ]]></command>
-    <inputs>
-        <param format="csv" name="substrates" type="data" label="Positive/Phosphorylated Substrate List"/>
-        <param format="csv" name="negatives" type="data" label="Negative/unPhosphorylated Substrate List"/>
-        <param format="csv" name="SBF" type="data" label="Substrate Background Frequency List"/>
-    </inputs>      
-    <outputs>
-        <data format="csv" name="SDtable" from_work_dir="output1.csv" label="Standard Deviation Table"/>
-        <data format="csv" name="EPM" from_work_dir="output2.csv" label="Endogenous Probability Matrix"/>
-        <data format="csv" name="Characterization" from_work_dir="output3.csv" label="Characterization Table"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="substrates" ftype="csv" value="substrates.csv"/>
-            <param name="negatives" ftype="csv" value="negatives.csv"/>
-            <param name="SBF" ftype="csv" value="SBF.csv"/>
-            <output name="SDtable" file="SDtable.csv"/>
-            <output name="EPM" file="EPM.csv"/>
-            <output name="Characterization" file="Characterization.csv"/>
-        </test>
-    </tests>
-
-    
-    <help><![CDATA[
-This tool is intended for use in conjunction with KinaMine.jar and Negative Motif Finder.  Using the outputs from those two functions (The Positive and Negative substrates as well as the Substrate Background Frequency) this tool calculates optimal substrates
-    ]]></help>
-    <citations>
-        <citation type="doi">10.1021/ja507164a</citation>
-    </citations>
-</tool>
-
+<tool id="kinatestid_r" name="Kinatest-ID 7_to_7" version="0.1.0">
+    <description>calculate optimal substrates</description>
+    <requirements>
+       <requirement type="package">R</requirement>
+    </requirements>
+    <command><![CDATA[
+        ln -s '$__tool_directory__/screener7-7.csv' screener &&
+        ln -s '$substrates' input1 && 
+        ln -s '$negatives' input2 && 
+        ln -s '$SBF' input3 &&
+        Rscript '$__tool_directory__/Kinatest-R_part1.R' &&
+        Rscript '$__tool_directory__/Kinatest-R_part2.R' &&
+        mv output1 output1.csv &&
+        mv output2 output2.csv &&
+        mv output3 output3.csv
+    ]]></command>
+    <inputs>
+        <param format="csv" name="substrates" type="data" label="Positive/Phosphorylated Substrate List"/>
+        <param format="csv" name="negatives" type="data" label="Negative/unPhosphorylated Substrate List"/>
+        <param format="csv" name="SBF" type="data" label="Substrate Background Frequency List"/>
+    </inputs>      
+    <outputs>
+        <data format="csv" name="SDtable" from_work_dir="output1.csv" label="Standard Deviation Table"/>
+        <data format="csv" name="EPM" from_work_dir="output2.csv" label="Endogenous Probability Matrix"/>
+        <data format="csv" name="Characterization" from_work_dir="output3.csv" label="Characterization Table"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="substrates" ftype="csv" value="substrates.csv"/>
+            <param name="negatives" ftype="csv" value="negatives.csv"/>
+            <param name="SBF" ftype="csv" value="SBF.csv"/>
+            <output name="SDtable" file="SDtable.csv"/>
+            <output name="EPM" file="EPM.csv"/>
+            <output name="Characterization" file="Characterization.csv"/>
+        </test>
+    </tests>
+
+    
+    <help><![CDATA[
+This tool is intended for use in conjunction with KinaMine.jar and Negative Motif Finder.  Using the outputs from those two functions (The Positive and Negative substrates as well as the Substrate Background Frequency) this tool calculates optimal substrates
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1021/ja507164a</citation>
+    </citations>
+</tool>
+